The research described in this application is a novel approach to the study of histone deacetylase enzymes (HDACs). These enzymes, which catalyze the removal of an acetyl group from the lysine residues of histone proteins, have recently been recognized to play an important role in the regulation of gene transcription, and have also been implicated in the suppression of some cancers. There are at least eight known human HDACs and five known yeast HDACs. Unfortunately, study of the specific targets and functions of the individual HDACs is hindered by a lack of selective inhibitors. The approach proposed involves engineering site-specific mutants of HDACs, thus creating molecular holes. Rationally designed inhibitors containing some extra steric bulk or "bumps" will then be synthesized to fit the mutant enzymes, thus creating specific inhibitors of individual HDACs. The engineered enzyme/inhibitor systems will then be inserted into cells to probe the effects of selective HDAC inhibition.